4IVD

JAK1 kinase (JH1 domain) in complex with compound 34


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Identification of C-2 Hydroxyethyl Imidazopyrrolopyridines as Potent JAK1 Inhibitors with Favorable Physicochemical Properties and High Selectivity over JAK2.

Zak, M.Hurley, C.A.Ward, S.I.Bergeron, P.Barrett, K.Balazs, M.Blair, W.S.Bull, R.Chakravarty, P.Chang, C.Crackett, P.Deshmukh, G.Devoss, J.Dragovich, P.S.Eigenbrot, C.Ellwood, C.Gaines, S.Ghilardi, N.Gibbons, P.Gradl, S.Gribling, P.Hamman, C.Harstad, E.Hewitt, P.Johnson, A.Johnson, T.Kenny, J.R.Koehler, M.F.Bir Kohli, P.Labadie, S.Lee, W.P.Liao, J.Liimatta, M.Mendonca, R.Narukulla, R.Pulk, R.Reeve, A.Savage, S.Shia, S.Steffek, M.Ubhayakar, S.van Abbema, A.Aliagas, I.Avitabile-Woo, B.Xiao, Y.Yang, J.Kulagowski, J.J.

(2013) J Med Chem 56: 4764-4785

  • DOI: 10.1021/jm4004895
  • Primary Citation of Related Structures:  
    4IVA, 4IVB, 4IVC, 4IVD

  • PubMed Abstract: 
  • Herein we report on the structure-based discovery of a C-2 hydroxyethyl moiety which provided consistently high levels of selectivity for JAK1 over JAK2 to the imidazopyrrolopyridine series of JAK1 inhibitors. X-ray structures of a C-2 hydroxyethyl analogue in complex with both JAK1 and JAK2 revealed differential ligand/protein interactions between the two isoforms and offered an explanation for the observed selectivity ...

    Herein we report on the structure-based discovery of a C-2 hydroxyethyl moiety which provided consistently high levels of selectivity for JAK1 over JAK2 to the imidazopyrrolopyridine series of JAK1 inhibitors. X-ray structures of a C-2 hydroxyethyl analogue in complex with both JAK1 and JAK2 revealed differential ligand/protein interactions between the two isoforms and offered an explanation for the observed selectivity. Analysis of historical data from related molecules was used to develop a set of physicochemical compound design parameters to impart desirable properties such as acceptable membrane permeability, potent whole blood activity, and a high degree of metabolic stability. This work culminated in the identification of a highly JAK1 selective compound (31) exhibiting favorable oral bioavailability across a range of preclinical species and robust efficacy in a rat CIA model.


    Organizational Affiliation

    Department of Discovery Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, USA. mzak@gene.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosine-protein kinase JAK1 AB302Homo sapiensMutation(s): 0 
Gene Names: JAK1JAK1AJAK1B
EC: 2.7.10.2
Find proteins for P23458 (Homo sapiens)
Explore P23458 
Go to UniProtKB:  P23458
NIH Common Fund Data Resources
PHAROS:  P23458
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
15T
Query on 15T

Download Ideal Coordinates CCD File 
A, B
3-(trans-4-{2-[(1R)-1-hydroxyethyl]imidazo[4,5-d]pyrrolo[2,3-b]pyridin-1(6H)-yl}cyclohexyl)propanenitrile
C19 H23 N5 O
LLRNGFSFYHDPKW-MGPQQGTHSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR
A,BL-PEPTIDE LINKINGC9 H12 N O6 PTYR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
15TEC50:  33   nM  BindingDB
15TKi:  0.30000001192092896   nM  Binding MOAD
15TKi:  0.30000001192092896   nM  BindingDB
15TKi :  0.30000001192092896   nM  PDBBind
15TEC50:  43   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.795α = 90
b = 173.608β = 94.53
c = 44.629γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-05-22
    Type: Initial release
  • Version 1.1: 2013-07-03
    Changes: Database references